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ksamuk / pixy

Software for painlessly estimating average nucleotide diversity within and between populations
https://pixy.readthedocs.io/
MIT License
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How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project #96

Closed JianhuaWang95 closed 6 months ago

JianhuaWang95 commented 7 months ago

Hi Kieran,

I want to use pixy to calculate the pi values for some genes using the vcf file downloaded from 1000 Genomes Project. I do not have the bam file, is there any other way that I can use to generate a vcf file with both invariant and variant sites?

Thanks, Jianhua

ksamuk commented 6 months ago

Hi Jianhua,

As far as a I know, it is not possible generate an allsites file without access to BAMs or gvcfs, apologies!

Kieran

JianhuaWang95 commented 6 months ago

Got it, thanks for the info!

Best, Jianhua

From: Kieran Samuk @.> Sent: Saturday, February 3, 2024 17:41 To: ksamuk/pixy @.> Cc: Wang, Jianhua @.>; Author @.> Subject: [EXTERNAL] Re: [ksamuk/pixy] How to generate a allsite vcf file based on the vcf file from 1000 Genomes Project (Issue #96)

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Hi Jianhua,

As far as a I know, it is not possible generate an allsites file without access to BAMs or gvcfs, apologies!

Kieran

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